1JJK | pdb_00001jjk

Selenomethionine Substitution of Orotidine-5'-monophosphate Decarboxylase from E. coli Causes a Change in Crystal Contacts and Space Group

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d1jjkc_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1jjkd_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G	d1jjkg_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
H	d1jjkh_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
I	d1jjki_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
J	d1jjkj_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
K	d1jjkk_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
L	d1jjkl_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
P	d1jjkp_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
O	d1jjko_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
N	d1jjkn_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
M	d1jjkm_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d1jjkf_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d1jjke_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1jjkb_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1jjka_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8043243	3000216	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8043243	3000216	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8043243	3000216	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8043243	3000216	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8043243	3000216	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8043243	3000216	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8043243	3000216	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8043243	3000216	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8043243	3000216	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8043243	3000216	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8043243	3000216	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8043243	3000216	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8043243	3000216	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8043243	3000216	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8043243	3000216	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8043243	3000216	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	NAD_binding_3	e1jjkC1	A: alpha arrays	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: C-terminal subdomain in Lon-related proteases catalytic domains	F: NAD_binding_3	ECOD (v295.2)
D	NAD_binding_3	e1jjkD1	A: alpha arrays	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: C-terminal subdomain in Lon-related proteases catalytic domains	F: NAD_binding_3	ECOD (v295.2)
G	NAD_binding_3	e1jjkG1	A: alpha arrays	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: C-terminal subdomain in Lon-related proteases catalytic domains	F: NAD_binding_3	ECOD (v295.2)
H	NAD_binding_3	e1jjkH1	A: alpha arrays	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: C-terminal subdomain in Lon-related proteases catalytic domains	F: NAD_binding_3	ECOD (v295.2)
I	NAD_binding_3	e1jjkI1	A: alpha arrays	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: C-terminal subdomain in Lon-related proteases catalytic domains	F: NAD_binding_3	ECOD (v295.2)
J	NAD_binding_3	e1jjkJ1	A: alpha arrays	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: C-terminal subdomain in Lon-related proteases catalytic domains	F: NAD_binding_3	ECOD (v295.2)
K	NAD_binding_3	e1jjkK1	A: alpha arrays	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: C-terminal subdomain in Lon-related proteases catalytic domains	F: NAD_binding_3	ECOD (v295.2)
L	NAD_binding_3	e1jjkL1	A: alpha arrays	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: C-terminal subdomain in Lon-related proteases catalytic domains	F: NAD_binding_3	ECOD (v295.2)
P	NAD_binding_3	e1jjkP1	A: alpha arrays	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: C-terminal subdomain in Lon-related proteases catalytic domains	F: NAD_binding_3	ECOD (v295.2)
O	NAD_binding_3	e1jjkO1	A: alpha arrays	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: C-terminal subdomain in Lon-related proteases catalytic domains	F: NAD_binding_3	ECOD (v295.2)
N	NAD_binding_3	e1jjkN1	A: alpha arrays	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: C-terminal subdomain in Lon-related proteases catalytic domains	F: NAD_binding_3	ECOD (v295.2)
M	NAD_binding_3	e1jjkM1	A: alpha arrays	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: C-terminal subdomain in Lon-related proteases catalytic domains	F: NAD_binding_3	ECOD (v295.2)
F	NAD_binding_3	e1jjkF1	A: alpha arrays	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: C-terminal subdomain in Lon-related proteases catalytic domains	F: NAD_binding_3	ECOD (v295.2)
E	NAD_binding_3	e1jjkE1	A: alpha arrays	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: C-terminal subdomain in Lon-related proteases catalytic domains	F: NAD_binding_3	ECOD (v295.2)
B	NAD_binding_3	e1jjkB1	A: alpha arrays	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: C-terminal subdomain in Lon-related proteases catalytic domains	F: NAD_binding_3	ECOD (v295.2)
A	NAD_binding_3	e1jjkA1	A: alpha arrays	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: C-terminal subdomain in Lon-related proteases catalytic domains	F: NAD_binding_3	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
D	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
G	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
H	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
I	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
J	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
K	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
L	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
P	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
O	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
N	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
M	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
F	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
E	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	PF00215	Orotidine 5'-phosphate decarboxylase / HUMPS family (OMPdecase)	Orotidine 5'-phosphate decarboxylase / HUMPS family	This family includes Orotidine 5'-phosphate decarboxylase enzymes EC:4.1.1.23 that are involved in the final step of pyrimidine biosynthesis. The family also includes enzymes such as hexulose-6-phosphate synthase. This family appears to be distantly ...	This family includes Orotidine 5'-phosphate decarboxylase enzymes EC:4.1.1.23 that are involved in the final step of pyrimidine biosynthesis. The family also includes enzymes such as hexulose-6-phosphate synthase. This family appears to be distantly related to Pfam:PF00834.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	OROTIDINE 5'-PHOSPHATE DECARBOXYLASE	carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity orotidine-5'-phosphate decarboxylase activity	nucleobase-containing compound metabolic process nucleobase-containing small molecule metabolic process small molecule metabolic process metabolic process cellular process primary metabolic process nucleobase-containing small molecule interconversion pyrimidine-containing compound metabolic process nucleobase biosynthetic process pyrimidine nucleobase biosynthetic process pyrimidine nucleobase metabolic process biosynthetic process nucleobase metabolic process 'de novo' pyrimidine nucleobase biosynthetic process nucleobase-containing compound metabolic process nucleobase-containing small molecule metabolic process small molecule metabolic process metabolic process cellular process primary metabolic process nucleobase-containing small molecule interconversion pyrimidine-containing compound metabolic process nucleobase biosynthetic process pyrimidine nucleobase biosynthetic process pyrimidine nucleobase metabolic process biosynthetic process nucleobase metabolic process 'de novo' pyrimidine nucleobase biosynthetic process pyrimidine-containing compound biosynthetic process ribose phosphate metabolic process nucleotide biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process 'de novo' UMP biosynthetic process ribonucleotide biosynthetic process UMP biosynthetic process ribonucleotide metabolic process UMP metabolic process phosphorus metabolic process nucleoside monophosphate metabolic process ribose phosphate biosynthetic process pyrimidine ribonucleotide metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process pyrimidine nucleoside monophosphate metabolic process pyrimidine ribonucleoside monophosphate metabolic process nucleobase-containing compound biosynthetic process nucleotide metabolic process nucleoside monophosphate biosynthetic process pyrimidine ribonucleoside monophosphate biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process pyrimidine nucleoside monophosphate biosynthetic process ribonucleoside monophosphate biosynthetic process pyrimidine nucleotide biosynthetic process pyrimidine ribonucleotide biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR047596	Orotidine 5'-phosphate decarboxylase, bacterial	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR001754	Orotidine 5'-phosphate decarboxylase domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR014732	Orotidine 5'-phosphate decarboxylase	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR018089	Orotidine 5'-phosphate decarboxylase, active site	Active Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR011060	Ribulose-phosphate binding barrel	Homologous Superfamily

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.